7t0u

Crystal structure of the BCL6 BTB domain in complex with OICR-12387

Method: X-RAY DIFFRACTION

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 2 of B-cell lymphoma 6 protein

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 1 GLYCEROL × 1 CHLORIDE ION × 2 ;3-chloro-5-{7-[2-({5-chloro-2-[(2S)-2-methyl-4-(oxetan-3-yl)piperazin-1-yl]pyridin-4-yl}amino)-2-oxoethyl]-3-methyl-4-oxo-2-(trifluoromethyl)-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl}-2-hydroxybenzamide ; × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 1 GLYCEROL × 1 CHLORIDE ION × 1 ;3-chloro-5-{7-[2-({5-chloro-2-[(2S)-2-methyl-4-(oxetan-3-yl)piperazin-1-yl]pyridin-4-yl}amino)-2-oxoethyl]-3-methyl-4-oxo-2-(trifluoromethyl)-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl}-2-hydroxybenzamide ; × 2 DIMETHYL SULFOXIDE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BCL6_HUMAN
Isoform	P41182-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–127； UniProt 5–129 Author chain B； PDBConstruct 3–127； UniProt 5–129 Author chain C； PDBConstruct 3–127； UniProt 5–129 Author chain D； PDBConstruct 3–127； UniProt 5–129

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7t0u
Deposition date deposition_date	2021-11-30
Structure title title	Crystal structure of the BCL6 BTB domain in complex with OICR-12387
Keywords keywords	immunity, inflammatory response, transcription repressor, TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex; TRANSCRIPTION/TRANSCRIPTION INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7t0u__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7t0u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7t0u__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.17 Å
Rg (electron density)	19.51 Å
Total Rg	20.45 Å
Atom count	4101
Residues	246
Excluded volume	36997 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7t0u__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7t0u__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Isoform 2 of B-cell lymphoma 6 protein
Molecular weight formula_weight	14559.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8925

GSADSQIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKRNLSVINLDPEINPEGFNILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTCRKFIKASE

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	;3-chloro-5-{7-[2-({5-chloro-2-[(2S)-2-methyl-4-(oxetan-3-yl)piperazin-1-yl]pyridin-4-yl}amino)-2-oxoethyl]-3-methyl-4-oxo-2-(trifluoromethyl)-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl}-2-hydroxybenzamide ;
Molecular weight formula_weight	709.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	349

▶

Unit-cell length a length_a	55.484 Å
Unit-cell length b length_b	72.545 Å
Unit-cell length c length_c	67.488 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.15 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	1.490 Å
Low-resolution limit resolution_low	36.270 Å
R factor r_factor	0.1425
R_work r_work	0.1406
R_free r_free	0.1799

Crystal structure of the BCL6 BTB domain in complex with OICR-12387

1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 2 of B-cell lymphoma 6 protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7t0u__assembly_1__model_1

7t0u__assembly_1__model_1 | I(q)

7t0u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Crystal structure of the BCL6 BTB domain in complex with OICR-12387

1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 2 of B-cell lymphoma 6 protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7t0u__assembly_1__model_1

7t0u__assembly_1__model_1 | I(q)

7t0u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)